Something they do for Milan-X parts.
4.5Ghz max turbo makes it an easier bin than the 5600X.
The part is a reclaim slot for the dregs that don't hit Milan-X bins.
Server CPUs typically take lower leakage (and thus lower max turbo) bins. If it gets rejected from Milan-X then it is usually because it is too leaky. Those too leaky CPUs shouldn't have a need for a reduced single core turbo though, only when lots of cores are loaded.
Maybe Milan-X bins are even tighter than Milan to try and get the most efficient dies to somewhat offset the increased power brought by the larger L3? Even if so, the CCD fabrication is separate from the V-cache so if they have CCDs that don't meat stricter Milan-X bins but still can be used for Milan, then why send them for 3d packaging in the first place? To this effect, there shouldn't be any Milan-X cast offs as the CCD will fail binning for Milan-X before being thinned and stacked. Maybe they aren't binning at all prior to stacking but that would seem very foolish and wasteful.
I think AMD's explanation makes the most sense. With the increased cost to produce, they are using the 5800x3d as a test case to see how the market reacts. This will have minimal disruption to their other lines and give AMD market feedback on 3d cache consumer products.